CD4 numbers in PBMC and tissues.

<p>Absolute CD4 counts in the blood of (A) untreated and (B) treated animals were plotted from multiple time points. (C) The percentage of CD4+ lymphocytes in PBMC, spleen and multiple lymph nodes taken at necropsy in 6 animals are shown.</p

MOESM1 of Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy

Additional file 1: Figure S1. RT-SHIV RNA copies detected by qRT-PCR in (A) plasma or (B) tissues of RT-SHIV infected animals at time of necropsy. The limit of detection of plasma viral RNA is 30 copies Eq/ml, indicated by the dashed line. The limit of detection of tissue viral RNA is 1 copy and was normalized per 106 CD4 copies. *indicates below the limit of detection; NA indicates that the sample was not available

The ratio of RT-SHIV <i>gag</i> DNA copies per 10⁶ macaque CCR5 DNA copies were measured in PBMC isolated at different time points from each of the untreated and treated macaques.

<p>The ratio of RT-SHIV <i>gag</i> DNA copies per 10⁶ macaque CCR5 DNA copies were measured in PBMC isolated at different time points from each of the untreated and treated macaques.</p

Plasma viremia was measured in all twelve macaques by qRT-PCR of RT-SHIV <i>gag</i> RNA.

<p>Animals were infected at week 0 and were (A) untreated or (B) treated with 3 or 4 antiretroviral drugs. Animals treated with 3 drugs (TFV, FTC, EFV) are denoted by closed symbols and treatment was initiated at week 10, denoted by the solid arrow. The animals treated with 4 drugs (TFV, FTC, EFV, and L-870812) are denoted by open symbols and treatment was initiated at week 13 (GV08 and GN19) or week 14 (GG45 and GV40), denoted by the open arrow. Treatment was continued daily until necropsy (week 30 or 31). The limit of detection of the assay was 30 vRNA copies/ml plasma.</p

MOESM1 of Rilpivirine analogs potently inhibit drug-resistant HIV-1 mutants

Additional file 1: Table S1–S4. The IC50 values (nM) of RPV and the RPV analogs were determined against the NNRTI resistant mutants were measured by using a single round infection assay, n = 4. The concentrations (nM) are measured by reductions in luciferase reporter activity followed by the standard deviations. In parenthesis is the fold-change that describes the difference between the IC50 value of the NNRTI resistant mutant relative to WT

MOESM2 of Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy

Additional file 2: Figure S2. Phylogenetic relationships between single-genome proviral env sequences obtained from various anatomical compartments 30 weeks post-infection from the untreated animal 6760. The env sequence populations in the tissues (open colored circles) were not significantly different from each other indicating that the virus is well circulated across compartments, consistent with the results from the pol analyses. Highly divergent sequences are G to A hypermutants

Lymphoid tissue viral DNA at necropsy is correlated with week 1 plasma viremia levels.

<p>(A) The ratio of <i>gag</i> copies per 10⁶ CCR5 copies for each tissue of the untreated RT-SHIV-infected macaques. The average of each qPCR reaction was used for the graph. In addition, the week 1 plasma viral load was included for each animal. Asterisks (*) denote samples that were not collected or in which no significant CCR5 DNA were measured. (B) The amount of <i>gag</i> vDNA detected in each of the lymphoid tissues for each animal was plotted against the week 1 plasma viremia level. Statistics determined a Spearman rank-order correlation of 0.996 with p value of < 0.0001.</p

The ratio of RT-SHIV <i>gag</i> RNA copies per 10⁶ macaque CD4 RNA copies were measured in PBMC isolated at week 1 or 2 and 28 or 30 post-infection from each of the untreated and treated macaques (black bars).

<p>The amount of RT-SHIV gag RNA in the plasma is also plotted for each animal at each time point (white bars). Asterisks (*) denote plasma viremia levels below the limit of detection (<30 copies/ml).</p

SIVRNA localizes with immune clusters in brain and spleen.

(A) Genes enriched in TEM and TCM clusters in control and SIV brain (p.adj B) UMAP of immune clusters in brain and vRNA expression in clusters in control and SIV. (C) UMAP of immune clusters in spleen and vRNA expression in clusters in control and SIV. Acute 251 (n = 4) cohort assessed. (TIF)</p

Gating strategy for CNS tissues in SIV unexposed controls.

Gating strategy for CNS tissues in SIV unexposed controls.</p